Thomas Eickermann

A new approach to measure single-event related brain activity using real-time fMRI: Feasibility of sensory, motor, and higher cognitive tasks

Real‐time fMRI is a rapidly emerging methodology that enables monitoring changes in brain activity during an ongoing experiment. In this article we demonstrate the feasibility of performing single‐event sensory, motor, and higher cognitive tasks in real‐time on a clinical whole‐body scanner. This approach requires sensitivity optimized fMRI methods: Using statistical parametric mapping we quantified the spatial extent of BOLD contrast signal changes as a function of voxel size and demonstrate that sacrificing spatial resolution and readout bandwidth improves the detection of signal changes in real time. Further increases in BOLD contrast sensitivity were obtained by using real‐time multi‐echo EPI. Real‐time image analysis was performed using our previously described Functional Imaging in REal time (FIRE) software package, which features real‐time motion compensation, sliding window correlation analysis, and automatic reference vector optimization. This new fMRI methodology was validated using single‐block design paradigms of standard visual, motor, and auditory tasks. Further, we demonstrate the sensitivity of this method for online detection of higher cognitive functions during a language task using single‐block design paradigms. Finally, we used single‐event fMRI to characterize the variability of the hemodynamic impulse response in primary and supplementary motor cortex in consecutive trials using single movements. Real‐time fMRI can improve reliability of clinical and research studies and offers new opportunities for studying higher cognitive functions. Hum. Brain Mapping 12:25–41, 2001.

Steering UNICORE applications with VISIT

The UNICORE (UNiform Interface to COmputing REsources) software provides a Grid infrastructure together with a computing portal for engineers and scientists to access supercomputer centres from anywhere on the Internet. While UNICORE is primarily designed for the submission and control of batch jobs, it is also feasible to establish an on-line connection between an application and the UNICORE user-client. This opens up the possibility of performing on-line visualization and computational steering of applications under UNICORE control while maintaining the security provided by this system. This contribution describes the design of a steering extension to UNICORE based on the steering toolkit VISIT (VISualization Interface Toolkit). VISIT is a lightweight library that supports bidirectional data exchange between visualizations and parallel applications. As an example application, a parallel simulation of a laser-plasma interaction that can be steered by an AVS/Express application is presented.

Reliable orchestration of distributed MPI-Applications in a UNICORE-Based grid with MetaMPICH and metascheduling

Running large MPI-applications with resource demands exceeding the local sites cluster capacity could be distributed across a number of clusters in a Grid instead, to satisfy the demand. However, there are a number of drawbacks limiting the applicability of this approach: communication paths between compute nodes of different clusters usually provide lower bandwidth and higher latency than the cluster internal ones, MPI libraries use dedicated I/O-nodes for inter-cluster communication which become a bottleneck, missing tools for co-ordinating the availability of the different clusters across different administrative domains is another issue. To make the Grid approach efficient several prerequisites must be in place: an implementation of MPI providing high-performance communication mechanisms across the borders of clusters, a network connection with high bandwidth and low latency dedicated to the application, compute nodes made available to the application exclusively, and finally a Grid middleware glueing together everything. In this paper we present work recently completed in the VIOLA project: MetaMPICH, user controlled QoS of clusters and interconnecting network, a MetaScheduling Service and the UNICORE integration.

Design and evaluation of a collaborative online visualization and steering framework implementation for computational grids

Todays large-scale scientific research often relies on the collaborative use of a Grid or c-Science infrastructure (e.g. DEISA, EGEE, TeraGrid, OSG) with computational, storage, or other types of physical resources. One of the goals of these emerging infrastructures is to support the work of scientists with advanced problem-solving tools. Many e-Science applications within these infrastructures aim at simulations of a scientific problem on powerful parallel computing resources. Typically, a researcher first performs a simulation for some fixed amount of time and then analyses results in a separate post-processing step, for instance, by viewing results in visualizations. In earlier work we have described early prototypes of a Collaborative Online Visualization and Steering (COVS) Framework in Grids that performs both -simulation and visualization -at the same time (online) to increase the efficiency of e-Scientists. This paper evaluates the evolved mature reference implementation of the COVS framework design that is ready for production usage within Web service-based Grid and e-Science infrastructures.

VISIT/GS: Higher Level Grid Services for Scientific Collaborative Online Visualization and Steering in UNICORE Grids

Many production Grid infrastructures such as DEISA, EGEE, or TeraGrid have begun to offer services to endusers that include access to computational resources. The major goal of these infrastructures is to facilitate the routine interaction of scientists and their workflows with advanced tools and seamless access to computational resources via Grid middleware systems such as UNICORE, gLite or Globus Toolkits. While UNICORE 5 is used in production Grids since several years, recently an early prototype of the new Web services-based UNICORE 6 became available that will be continuously improved in the next months for its use in production. In absence of a widely accepted framework for visualization and steering, the new UNICORE 6 Grid middleware provides not such a higher level service by default. This motivates this contribution to support e-Scientists in upcoming WS-based UNICORE Grids with visualization and steering techniques. In this paper we present the augmentation of the early standards-based UNICORE 6 prototype with a higher-level service for collaborative online visualization and steering. It describes the seamless integration of this service within UNICORE Grids by retaining the convenient single sign-on feature.

Metacomputing in gigabit environments: networks, tools, and applications

Abstract This article gives an overview over recent and current metacomputing activities of the Computing Centers at the Forschungszentrum Julich, the GMD Forschungszentrum Informationstechnik and the University of Stuttgart. It starts with a discussion of the underlying network connections which are dedicated testbeds. A library that provides an MPI-API for metacomputing applications is presented, as well as a library that supports load-balancing and latency hiding. Finally, results from several applications ranging from tightly coupled homogeneous to loosely coupled heterogeneous metacomputing are presented.

Computational Steering and Online Visualization of Scientific Applications on Large-Scale HPC Systems within e-Science Infrastructures

In the past several years, many scientific applications from various domains have taken advantage of e-science infrastructures that share storage or computational resources such as supercomputers, clusters or PC server farms across multiple organizations. Especially within e-science infrastructures driven by high-performance computing (HPC) such as DEISA, online visualization and computational steering (COVS) has become an important technique to save compute time on shared resources by dynamically steering the parameters of a parallel simulation. This paper argues that future supercomputers in the Petaflop/s performance range with up to 1 million CPUs will create an even stronger demand for seamless computational steering technologies. We discuss upcoming challenges for the development of scalable HPC applications and limits of future storage/IO technologies in the context of next generation e- science infrastructures and outline potential solutions.

Extending the collaborative online visualization and steering framework for computational Grids with attribute-based authorization

Especially within grid infrastructures driven by high-performance computing (HPC), collaborative online visualization and steering (COVS) has become an important technique to dynamically steer the parameters of a parallel simulation or to just share the outcome of simulations via visualizations with geographically dispersed collaborators. In earlier work, we have presented a COVS framework reference implementation based on the UNICORE grid middleware used within DEISA. This paper lists current limitations of the COVS framework design and implementation related to missing fine-grained authorization capabilities that are required during collaborative COVS sessions. Such capabilities use end-user information about roles, project membership, or participation in a dedicated virtual organization (VO). We outline solutions and present a design and implementation of our architecture extension that uses attribute authorities such as the recently developed virtual organization membership service (VOMS) based on the security assertion markup language (SAML).

Performance Issues of Distributed MPI Applications in a German Gigabit Testbed

The Gigabit Testbed West is a testbed for the planned upgrade of the German Scientific Network B-WiN. It is based on a 2.4 Gigabit/second ATM connection between the Research Centre Julich and the GMD - National Research Center for Information Technology in Sankt Augustin. This contribution reports on those activities in the testbed that are related to metacomputing. It starts with a discussion of the IP connectivity of the supercomputers in the testbed. The achieved performance is compared with MetaMPI, an MPI library that is tuned for the use in metacomputing environments with high-speed networks. Applications using this library are briefly described.

Distributed collaborative data analysis with heterogeneous visualisation systems

A system for the distributed, collaborative online visualisation in heterogeneous visualisation environments was developed and tested in the application project KoDaVis, which is part of the german optical network testbed VIOLA. The aim of KoDaVis is the visualisation of huge data sets from atmosphere research. The core of the presented distributed computer supported collaborative work system is a framework for the coupling of heterogeneous visualisation systems and the design and implementation of two distinct servers, one for the collaborative aspects and one for the direct remote access to centrally stored data. Interfaces to the VTK-based virtual reality visualisation system ViSTA and to the modular visualisation environment AVS/Express were implemented and tested. The successful coupling of these two different visualisation systems as well as the benefit of a fast optical network for parallel data access and for distributed collaboration could be demonstrated in a test setup.